Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes
Joint Authors
Schreiner, Wolfgang
Ribarics, Reiner
Ilieva, Nevena
Kenn, Michael
Karch, Rudolf
Source
Journal of Immunology Research
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-20, 20 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-11-05
Country of Publication
Egypt
No. of Pages
20
Main Subjects
Abstract EN
MHC α-helices form the antigen-binding cleft and are of particular interest for immunological reactions.
To monitor these helices in molecular dynamics simulations, we applied a parsimonious fragment-fitting method to trace the axes of the α-helices.
Each resulting axis was fitted by polynomials in a least-squares sense and the curvature integral was computed.
To find the appropriate polynomial degree, the method was tested on two artificially modelled helices, one performing a bending movement and another a hinge movement.
We found that second-order polynomials retrieve predefined parameters of helical motion with minimal relative error.
From MD simulations we selected those parts of α-helices that were stable and also close to the TCR/MHC interface.
We monitored the curvature integral, generated a ruled surface between the two MHC α-helices, and computed interhelical area and surface torsion, as they changed over time.
We found that MHC α-helices undergo rapid but small changes in conformation.
The curvature integral of helices proved to be a sensitive measure, which was closely related to changes in shape over time as confirmed by RMSD analysis.
We speculate that small changes in the conformation of individual MHC α-helices are part of the intrinsic dynamics induced by engagement with the TCR.
American Psychological Association (APA)
Ribarics, Reiner& Kenn, Michael& Karch, Rudolf& Ilieva, Nevena& Schreiner, Wolfgang. 2015. Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes. Journal of Immunology Research،Vol. 2015, no. 2015, pp.1-20.
https://search.emarefa.net/detail/BIM-1068386
Modern Language Association (MLA)
Ribarics, Reiner…[et al.]. Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes. Journal of Immunology Research No. 2015 (2015), pp.1-20.
https://search.emarefa.net/detail/BIM-1068386
American Medical Association (AMA)
Ribarics, Reiner& Kenn, Michael& Karch, Rudolf& Ilieva, Nevena& Schreiner, Wolfgang. Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes. Journal of Immunology Research. 2015. Vol. 2015, no. 2015, pp.1-20.
https://search.emarefa.net/detail/BIM-1068386
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1068386